you are right, I think also that a mother can find an other mean to be informed by a doctot about the health of her son than to be present in the exam room.
At least, she can leave the exam room when it is time to the the most intimate part of the exam generally at the end of the physicals or she can turn her head away.
the doctor has also a responsability in protecting the privacy of the teenagers that he is examining, he can have set a curtain in the exam room behind it he performed the most intimate part of the exam.
Anyway, there cannot be a general rule for all persons and cases, some teenagers may prefer to have a parent in the exam room, particularly their mother who cares very well about their health because they are anxious if they are really sick, it is not the same situations as for a routine annual physical.
it may depend also of the age, under 12, it is not too much embarrassing to have a mother in the exam room, between 12 and 14 age, it may depend on the character of the boy, if he is already enough mature.
after 14 age, it would be more seldom.
but we cannot forget that the boys are generally less mature than the girls, so the parents must care much about their son than a daughter and it is still the mother in most of the families who cares about the health of the children whatever is their age.
the good solution is a question of good sense, everybody can understand when a mother must not be present or what must be her behaviour, a discreet one, in the exam room.